Transplanting into a Hydroponic System

Transplanting into a Hydroponic System

Now that your seeds are germinated, you’re probably asking, “Ok, but how do I get my seedling into my hydroponic system?” Regardless of what type of system or substrate you’ll be using, the process is basically the same. The same method can also be used for transplanting rooted clones.

For simplicity, we will be discussing how to transplant seedlings into a single plant DWC system with LECA (Light Expanded Clay Aggregate) from coco coir. DWC stands for Deep Water Culture, it consists of a plant that has roots suspended in aerated, nutrient-rich water. For beginners, we recommend using something like an EZPonix Grow System, which is easy to set up and use, and provides faster growth than soil.

Graphic on green background showing a 5 gallon bucket with an air pump and air stone


Preparing your System

Before you get started, you’ll want to prepare your system and grow medium. Attach your air stone to one end of the tubing, and through a pre-drilled hole near the top of your reservoir, with the air stone on the inside. Now, attach the other end of the tubing to your air pump on the outside of the reservoir. Your air pump should be located above your reservoir to prevent water from being pulled back into the pump if you lose power.

Add your pre-mixed nutrients to the reservoir so that the water level is just below the bottom of the net cup. At this level, the air stone will cause the water to splash up to the roots, but not completely submerge them. The roots stay damp, and the increased oxygen encourages healthy root growth.

The last step before you transplant, is to rinse your LECA. This step also applies if you are using perlite. Rinsing the media removes dust that could clog pumps or roots, and keeps your system clean. You can rinse it by placing it in a net cup or colander, then set aside in a cup or other easily pourable container.

Transplanting your Seedling

Hands holding a square plug of coco coir, with pepper seedlings coming out of the top.

Start by carefully pushing up on the bottom of the seed tray to remove your seedling and coco. Begin gently bruising the coco coir away from the roots. While the roots are delicate and should be handled carefully, you shouldn't be afraid to touch them. When you’ve removed most of the coco coir, dunk the roots in a cup of water to wash off the rest.

Hands holding a seedling over a cup of water, and gently removing coco coir from the roots

Taking your net cup, hold your seedling so the roots are close to the bottom. Depending on the length of the roots, they may go through the bottom, or be just above it. It’s important to make sure the leaves are at least to the top of the net cup. Now you can begin adding your LECA around the sides until the seedling is standing on its own and the stem of the plant is mostly above the LECA.

hands holding a seedling in a net cup

With your system set up and your seedling transplanted, you can put the net cup into your system. You’ll need to check the water level once or twice a day to make sure the roots aren’t drying out.


For a video tutorial of this process, visit Taproot Hydroponics Atlanta on YouTube. We’re here to answer your questions. Reach out to us on chat, or stop by Taproot Hydroponics & Organics for personalized service and hydroponic system consultations.

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